Contacts of the helix formed by residues 397 - 407 (chain A) in PDB entry 3L6X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A LEU 3.5 21.8 + - - +
394A CYS 3.0 8.8 + - - +
395A TYR 3.8 2.7 - - - +
396A ARG* 1.3 78.9 + - - +
398A ASP* 1.3 66.1 + - - +
399A LYS* 3.5 10.9 + - - +
400A VAL* 3.0 42.9 + - + +
401A LYS* 3.1 12.9 + - - +
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ARG 4.0 1.2 + - - -
397A ASN* 1.3 72.1 - - - +
399A LYS* 1.3 63.6 + - - +
401A LYS* 3.2 17.0 + - - +
402A THR* 3.0 27.2 + - - +
438A GLY* 3.9 10.0 - - - -
439A ARG* 3.7 28.5 + - - +
440A ASP* 4.9 6.3 + - + +
443A ASN* 4.8 0.6 + - - +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASN* 3.2 9.7 + - - +
398A ASP* 1.3 77.1 - - - +
400A VAL* 1.3 65.2 + - + +
402A THR* 3.1 8.1 + - - -
403A ASP* 2.9 32.7 + - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 4.4 15.7 - - + -
393A LEU* 3.8 33.4 - - + +
394A CYS* 3.9 16.2 - - - -
397A ASN* 3.0 34.3 + - - +
399A LYS* 1.3 75.7 - - + +
401A LYS* 1.3 64.5 + - - +
403A ASP* 3.1 9.9 + - - +
404A VAL* 2.9 28.7 + - + +
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Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A CYS* 3.0 44.2 - - + -
396A ARG* 4.6 0.4 - - - +
397A ASN 3.1 16.1 + - - +
398A ASP* 3.4 17.0 + - - +
400A VAL* 1.3 77.6 - - - +
402A THR* 1.3 61.8 + - - +
404A VAL* 3.3 5.5 + - - +
405A ARG* 3.2 15.2 + - - +
434A ASN 2.8 30.0 + - - +
435A ILE* 4.1 13.8 - - - +
437A PHE* 2.9 25.1 + - - +
438A GLY* 4.7 1.4 - - - -
443A ASN* 3.4 25.5 + - - +
764B GLU* 2.7 26.8 + - - -
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Residues in contact with THR 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP* 3.0 13.3 + - - +
399A LYS* 3.1 9.4 + - - -
401A LYS* 1.3 73.2 - - - +
403A ASP* 1.3 68.5 + - - +
405A ARG* 3.2 10.1 + - - +
406A LYS* 3.1 48.2 + - + +
440A ASP* 2.6 36.7 + - - +
443A ASN* 3.8 7.9 + - - -
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Residues in contact with ASP 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 3.5 22.9 - - + +
399A LYS* 2.9 21.6 + - - +
400A VAL* 3.6 6.9 - - - +
402A THR* 1.3 79.4 - - - +
404A VAL* 1.3 56.9 + - - +
406A LYS* 3.1 13.9 + - - +
407A LEU* 2.8 39.0 + - + +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 4.2 11.9 - - + -
372A ILE* 4.2 12.3 - - + -
390A LEU* 4.1 31.0 - - + -
394A CYS* 4.1 14.6 - - - -
400A VAL* 2.9 20.1 + - + +
401A LYS 3.6 7.9 - - - +
402A THR 3.3 0.2 - - - -
403A ASP* 1.3 75.3 - - - +
405A ARG* 1.3 61.6 + - - +
407A LEU* 3.4 1.2 + - - +
408A LYS 3.2 2.9 + - - -
409A GLY* 2.8 48.5 + - - -
410A ILE* 4.5 3.1 - - + +
413A LEU* 4.5 0.4 - - + -
435A ILE* 3.8 22.7 - - + -
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LYS 3.2 3.0 + - - +
402A THR* 3.2 17.8 + - - +
404A VAL* 1.3 78.3 - - - +
406A LYS* 1.3 82.4 + - - +
408A LYS* 2.8 23.2 + - - +
410A ILE* 3.9 24.4 + - + +
411A PRO* 5.9 0.2 - - - +
440A ASP* 2.6 28.7 + - - -
442A ASP* 3.5 42.9 + - - +
443A ASN* 2.6 44.1 + - - +
446A ALA* 3.9 12.8 - - + -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A THR* 3.1 35.0 + - + +
403A ASP* 3.1 15.4 + - - +
405A ARG* 1.3 90.6 - - + +
407A LEU* 1.3 61.4 + - + +
408A LYS* 2.9 16.6 + - - +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 3.8 34.3 - - + -
369A PRO* 4.2 24.7 - - + -
372A ILE* 3.6 32.4 - - + +
403A ASP* 2.8 21.8 + - + +
404A VAL 3.9 0.2 - - - +
406A LYS* 1.3 77.9 - - + +
408A LYS* 1.3 72.5 + - - +
409A GLY* 3.3 0.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il